Digital expression profiling of novel diatom transcripts provides insight into their biological functions

We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity.The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.In the current catalogue of eight major groups of eukaryotic taxa [1], the majority of well explored model organisms belong to the plant (Archaeplastida) and the animal (Opisthokonta) groups, which both evolved from primary endosymbiotic events that generated chloroplasts and mitochondria. The heterokonts, on the other hand, probably evolved from serial secondary endosymbiosis events in which a heterotrophic eukaryote engulfed both autotrophic red and green eukaryotic algae [2-4]. As a consequence, these organisms derive from the combination of three distinct nuclear genomes. The group includes highly diverse, ecologically important photosynthetic groups, such as diatoms,